This overview presents the different water masses present in the various primary and secondary marine regions of the Mediterranean Sea and Black Sea, providing information on their main physical characteristics (i.e., temperature, salinity, density), the water depths at which they have been observed and the processes involved in their formation. There is a characteristic difference in the overall hydrology of the Mediterranean Sea compared to the Black Sea, in terms of the number and characteristics of water masses and their formation processes, although they form a single (integrated) marine system. This difference is explained by the limited communication between the two seas through the Sea of Marmara and its straits (the Dardanelles and Bosporus) and by the fact that the Mediterranean Sea is a condensation basin while the Black Sea is a dilution basin; therefore, the deficit of water in the former is compensated by the inflow of Atlantic waters, while the surplus in the latter outflows to the Aegean Sea. In total, 21 different water masses have been identified in the Mediterranean Sea (excluding the Straits of Gibraltar and the Sea of Marmara) compared to the 5 water masses identified in the Black Sea (excluding the Sea of Azov). This large number of water masses is attributed to coastal morphology (i.e., presence of straits) and submarine relief (i.e., deep basin separated by shallow sills) and different formation processes.